Journal of Biology


Open Access Highly Access

Evidence for large domains of similarly expressed genes in the Drosophila genome

Paul T Spellman* and Gerald M Rubin

Journal of Biology 2002, 1:5 doi:10.1186/1475-4924-1-5

Accesses  

  • Last 30 days: 91 accesses
  • Last year: 1222 accesses
  • All time: 34760 accesses

Cited by

BioMed Central: 50 citations

Research   Open Access Highly Accessed

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

Sean Thomas, Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos Genome Biology 2011, 12:R43 (11 May 2011)

A map of the dynamically changing chromatin landscape throughout Drosophila development.

Research article   Open Access

Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture

Shuwei Li, Ching-Hua Shih, Michael H Kohn BMC Genomics 2010, 11:322 (24 May 2010)

Research   Open Access

Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression

Oleg V Grinchuk, Efthimios Motakis, Vladimir A Kuznetsov BMC Genomics 2010, 11(Suppl 1):S9 (10 February 2010)

Research   Open Access Highly Accessed

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009)

The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes.

Research   Open Access

Microarray data mining using Bioconductor packages

Haisheng Nie, Pieter BT Neerincx, Jan Poel, Francesco Ferrari, Silvio Bicciato, Jack AM Leunissen, Martien AM Groenen BMC Proceedings 2009, 3(Suppl 4):S9 (16 July 2009)

Research   Open Access Highly Accessed

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler Genome Biology 2009, 10:R73 (9 July 2009)

A map of transcription start sites across the Drosophila genome, providing insights into initiation patterns and spatiotemporal conditions.

Research article   Open Access

Cooperation between NRF-2 and YY-1 transcription factors is essential for triggering the expression of the PREPL-C2ORF34 bidirectional gene pair

Chien-Chang Huang, Wun-Shaing Chang BMC Molecular Biology 2009, 10:67 (3 July 2009)

Research article   Open Access

A comparative analysis of divergently-paired genes (DPGs) among Drosophila and vertebrate genomes

Liang Yang, Jun Yu BMC Evolutionary Biology 2009, 9:55 (11 March 2009)

Research   Open Access

Searching for bidirectional promoters in Arabidopsis thaliana

Quan Wang, Lin Wan, Dayong Li, Lihuang Zhu, Minping Qian, Minghua Deng BMC Bioinformatics 2009, 10(Suppl 1):S29 (30 January 2009)

Research article   Open Access Highly Accessed

Positive correlation between gene coexpression and positional clustering in the zebrafish genome

Yen Kaow Ng, Wei Wu, Louxin Zhang BMC Genomics 2009, 10:42 (22 January 2009)

Research article   Open Access

Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

Qianqian Zhu, Marc S Halfon BMC Genomics 2009, 10:9 (7 January 2009)

Research   Open Access Highly Accessed

Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution

Carlos Quijano, Pavel Tomancak, Jesus Lopez-Marti, Mikita Suyama, Peer Bork, Marco Milan, David Torrents, Miguel Manzanares Genome Biology 2008, 9:R176 (16 December 2008)

Genes occurring in conserved, tandemly-arrayed clusters in Drosophila melanogaster are co-expressed to a much higher extent than other duplicated genes.

Research   Open Access Highly Accessed

Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila

Enrique Blanco, Miguel Pignatelli, Sergi Beltran, Adrià Punset, Silvia Pérez-Lluch, Florenci Serras, Roderic Guigó, Montserrat Corominas Genome Biology 2008, 9:R134 (10 September 2008)

Transcriptional analysis of chromatin regulator mutants in Drosophila melanogaster identified clusters of functionally related genes conserved in other insect species.

Research article   Open Access Highly Accessed

Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

Wilfried Haerty, Carlo Artieri, Navid Khezri, Rama S Singh, Bhagwati P Gupta BMC Genomics 2008, 9:399 (27 August 2008)

Technical Note   Open Access

SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences

Márcia A Inda, Marinus F van Batenburg, Marco Roos, Adam SZ Belloum, Dmitry Vasunin, Adianto Wibisono, Antoine HC van Kampen, Timo M Breit BMC Research Notes 2008, 1:63 (8 August 2008)

Minireview   Free Highly Accessed

Genomics technology for assessing soil pollution

Nico M van Straalen, Dick Roelofs Journal of Biology 2008, 7:19 (14 July 2008)

Research article   Open Access

Topoisomerase II inhibition involves characteristic chromosomal expression patterns

Susanne Reymann, Jürgen Borlak BMC Genomics 2008, 9:324 (8 July 2008)

Research article   Open Access

Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome

Jason G Mezey, Sergey V Nuzhdin, Fangfei Ye, Corbin D Jones BMC Evolutionary Biology 2008, 8:2 (7 January 2008)

Research article   Open Access

Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system

Huai-Kuang Tsai, Cindy PC Su, Mei-Yeh J Lu, Ching-Hua Shih, Daryi Wang BMC Genomics 2007, 8:352 (3 October 2007)

Software   Open Access

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

Jeremiah J Faith, Andrew J Olson, Timothy S Gardner, Ravi Sachidanandam BMC Bioinformatics 2007, 8:344 (18 September 2007)

Research   Open Access Highly Accessed

Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila

Boris Adryan, Gertrud Woerfel, Ian Birch-Machin, Shan Gao, Marie Quick, Lisa Meadows, Steven Russell, Robert White Genome Biology 2007, 8:R167 (16 August 2007)

An analysis of Drosophila Su(Hw) binding allowed the identification of new, isolated, binding sites, and the construction of a new binding site consensus. Together with gene expression data, this supports a role for Su(Hw) in maintaining a constant genomic architecture.

Editorial   Open Access Highly Accessed

Journal of Biology celebrates its fifth anniversary

Journal of Biology 2007, 6:5 (29 June 2007)

Research   Open Access

Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae

Birgitte Regenberg, Thomas Grotkjær, Ole Winther, Anders Fausbøll, Mats Åkesson, Christoffer Bro, Lars Hansen, Søren Brunak, Jens Nielsen Genome Biology 2006, 7:R107 (14 November 2006)

Analysis of S. cerevisiae cultures with generation times varying between 2 and 35 hours shows that the expression of half of all yeast genes is affected by the specific growth rate.

Software   Open Access

REEF: searching REgionally Enriched Features in genomes

Alessandro Coppe, Gian Antonio Danieli, Stefania Bortoluzzi BMC Bioinformatics 2006, 7:453 (16 October 2006)

Proceedings   Open Access

GOFFA: Gene Ontology For Functional Analysis – A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data

Hongmei Sun, Hong Fang, Tao Chen, Roger Perkins, Weida Tong BMC Bioinformatics 2006, 7(Suppl 2):S23 (26 September 2006)

Research article   Open Access

Transcriptome profiling of human hepatocytes treated with Aroclor 1254 reveals transcription factor regulatory networks and clusters of regulated genes

Susanne Reymann, Jürgen Borlak BMC Genomics 2006, 7:217 (26 August 2006)

Research article   Open Access

Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome

Debra T Burhans, Lakshmi Ramachandran, Jianxin Wang, Ping Liang, Hugh G Patterton, Michael Breitenbach, William C Burhans BMC Evolutionary Biology 2006, 6:58 (21 July 2006)

Research   Open Access Highly Accessed

Comparative genomics of Drosophila and human core promoters

Peter C FitzGerald, David Sturgill, Andrey Shyakhtenko, Brian Oliver, Charles Vinson Genome Biology 2006, 7:R53 (7 July 2006)

Comparison of DNA sequence distributions in Drosophila and human promoters suggests that different motifs have distinct functional roles.

Research article   Open Access Highly Accessed

Transcriptome coexpression map of human embryonic stem cells

Huai Li, Ying Liu, Soojung Shin, Yu Sun, Jeanne F Loring, Mark P Mattson, Mahendra S Rao, Ming Zhan1 BMC Genomics 2006, 7:103 (2 May 2006)

Expression profiling of human embryonic stem cells (ES) and embryoid bodies (EB), the earliest stage of ES differentiation, identifies specific chromosomal domains with coexpressing neighboring genes that differ between ES and EB in coexpression pattern.

Methodology article   Open Access

Operon information improves gene expression estimation for cDNA microarrays

Guanghua Xiao, Betsy Martinez-Vaz, Wei Pan, Arkady B Khodursky BMC Genomics 2006, 7:87 (21 April 2006)

Research   Open Access Highly Accessed

Molecular processes during fat cell development revealed by gene expression profiling and functional annotation

Hubert Hackl, Thomas Burkard, Alexander Sturn, Renee Rubio, Alexander Schleiffer, Sun Tian, John Quackenbush, Frank Eisenhaber, Zlatko Trajanoski Genome Biology 2005, 6:R108 (19 December 2005)

In-depth bioinformatics analyses of expressed sequence tags found to be differentially expressed during differentiation of 3T3-L1 pre-adipocyte cells were combined with de novo functional annotation and mapping onto known pathways to generate a molecular atlas of fat-cell development.

Research article   Open Access

Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome

Laurence D Hurst, Martin J Lercher BMC Evolutionary Biology 2005, 5:62 (8 November 2005)

Research article   Open Access Highly Accessed

Chromosomal clustering of a human transcriptome reveals regulatory background

Jan H Vogel, Anja von Heydebreck, Antje Purmann, Silke Sperling BMC Bioinformatics 2005, 6:230 (19 September 2005)

Review   Free

A non-random walk through the genome

Brian Oliver, Tom Misteli Genome Biology 2005, 6:214 (31 March 2005)

Genes showing particular expression patterns are not randomly distributed in the genome but are clustered into neighborhoods. This organization may be related to chromatin and the structure of the nucleus.

Research article   Open Access

Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains

Liang Chen, Hongyu Zhao BMC Genomics 2005, 6:44 (23 March 2005)

Research article   Open Access

Global transcriptome analysis of the C57BL/6J mouse testis by SAGE: evidence for nonrandom gene order

Petr Divina, Čestmír Vlček, Petr Strnad, Václav Pačes, Jiří Forejt BMC Genomics 2005, 6:29 (5 March 2005)

Research   Open Access

Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae

Gaetano Tripoli, Domenica D'Elia, Paolo Barsanti, Corrado Caggese Genome Biology 2005, 6:R11 (31 January 2005)

An analysis of nuclear-encoded oxidative phosphorylation genes in Drosophila and Anopheles reveals that pairs of duplicated genes have strikingly different expression patterns.

Methodology article   Open Access

Modelling the correlation between the activities of adjacent genes in drosophila

Helene H Thygesen, Aeilko H Zwinderman BMC Bioinformatics 2005, 6:10 (19 January 2005)

Research article   Open Access

Genome-scale analysis of positional clustering of mouse testis-specific genes

Quan Li, Bernett TK Lee, Louxin Zhang BMC Genomics 2005, 6:7 (19 January 2005)

Methodology article   Open Access Highly Accessed

CLOE: Identification of putative functional relationships among genes by comparison of expression profiles between two species

Maurizio Pellegrino, Paolo Provero, Lorenzo Silengo, Ferdinando Di Cunto BMC Bioinformatics 2004, 5:179 (19 November 2004)

Research   Open Access

Spatial patterns of transcriptional activity in the chromosome of Escherichia coli

Kyeong Jeong, Jaeyong Ahn, Arkady B Khodursky Genome Biology 2004, 5:R86 (27 October 2004)

Analysis of the transcriptional activity in Escherichia coli K12 revealed an asymmetry in the distribution of transcriptional patterns along the bacterial chromosome and showed that spatial patterns of transcription could be modulated pharmacologically and genetically.

Research   Open Access Highly Accessed

A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults

Michael Parisi, Rachel Nuttall, Pamela Edwards, James Minor, Daniel Naiman, Jining Lü, Michael Doctolero, Marina Vainer, Cathy Chan, James Malley, Scott Eastman, Brian Oliver Genome Biology 2004, 5:R40 (1 June 2004)

A global analysis of sex-biased transcription in Drosophila shows extensive differential expression between the sexes. Most sex-differential expression is due to germ cells and nearly all genes with germline expression show sex-bias.

Research   Open Access Highly Accessed

The regulatory content of intergenic DNA shapes genome architecture

Craig E Nelson, Bradley M Hersh, Sean B Carroll Genome Biology 2004, 5:R25 (15 March 2004)

The relationship between regulatory complexity and gene spacing was examined in Caenorhabditis elegans and Drosophila melanogaster. Intergenic distance, and hence genome architecture, is shaped by regulatory information contained in noncoding DNA.

Research article   Open Access

Inter-species differences of co-expression of neighboring genes in eukaryotic genomes

Yutaka Fukuoka, Hidenori Inaoka, Isaac S Kohane BMC Genomics 2004, 5:4 (13 January 2004)

Deposited research article   Free

Positional clustering of differentially expressed genes on human chromosomes 20, 21 and 22

Karine Mégy, Stéphane Audic, Jean-Michel Claverie Genome Biology 2003, 4:P1 (10 January 2003)

The relationship between gene co-expression and chromosomal co-localization in the human genome is expolored by analyzing the expression status of the genes along the best-annotated chromosomes 20, 21 and 22.

Research news   Free

Gene clusters in the fly genome

Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021213-01 (13 December 2002)

Testis-specific genes in Drosophila are often located in genomic clusters.

Minireview   Free

Variations in abundance: genome-wide responses to genetic variation... and vice versa

Bruce A Hamilton Genome Biology 2002, 3:reviews1029-reviews1029.3 (19 September 2002)

How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern.

Research news   Free

Muscling in on chromosomal clusters

Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020902-01 (2 September 2002)

Genes expressed in worm muscle are found in clusters throughout the genome.

Minireview   Free Highly Accessed

Gene expression neighborhoods

Brian Oliver, Michael Parisi, David Clark Journal of Biology 2002, 1:4 (1 July 2002)

Research news   Free

Transcriptional territories in the genome

Jonathan B Weitzman Journal of Biology 2002, 1:2 (25 June 2002)